On 05/08/2012 01:36 PM, Lucas Nussbaum wrote: > Source: bowtie2 > Version: 2.0.0-beta5-1 > Severity: serious > Tags: wheezy sid > User: debian...@lists.debian.org > Usertags: qa-ftbfs-20120508 qa-ftbfs > Justification: FTBFS on amd64 > > Hi, > > During a rebuild of all packages in sid, your package failed to build on > amd64. > > Relevant part: > >> /usr/bin/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 >> -m64 -msse2 -funroll-loops -g3 \"" \ >> -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" >> -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" >> -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" >> -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_PTHREADS >> -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ >> \ >> -o bowtie2-build bt2_build.cpp \ >> ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp >> bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp >> diff_sample.cpp bowtie_build_main.cpp \ >> >> In file included from bt2_idx.h:45:0, >> from bt2_build.cpp:27: >> word_io.h: In function 'uint32_t readU32(int, bool)': >> word_io.h:86:27: error: 'read' was not declared in this scope >> word_io.h: In function 'uint32_t readI32(int, bool)': >> word_io.h:134:27: error: 'read' was not declared in this scope >> In file included from bt2_idx.h:47:0, >> from bt2_build.cpp:27: >> ref_read.h: In constructor 'RefRecord::RefRecord(int, bool)': >> ref_read.h:69:21: error: 'read' was not declared in this scope >> In file included from bt2_build.cpp:27:0: >> bt2_idx.h: In destructor 'Ebwt::~Ebwt()': >> bt2_idx.h:927:3: error: 'close' was not declared in this scope >> bt2_idx.h:928:3: error: 'close' was not declared in this scope >> In file included from ref_read.h:32:0, >> from ref_read.cpp:20: >> word_io.h: In function 'uint32_t readU32(int, bool)': >> word_io.h:86:27: error: 'read' was not declared in this scope >> word_io.h: In function 'uint32_t readI32(int, bool)': >> word_io.h:134:27: error: 'read' was not declared in this scope >> In file included from ref_read.cpp:20:0: >> ref_read.h: In constructor 'RefRecord::RefRecord(int, bool)': >> ref_read.h:69:21: error: 'read' was not declared in this scope >> edit.cpp: In static member function 'static void >> Edit::printQAlign(std::ostream&, const char*, const BTDnaString&, const >> EList<Edit>&)': >> edit.cpp:100:8: warning: variable 'ins' set but not used >> [-Wunused-but-set-variable] >> edit.cpp:124:8: warning: variable 'ins' set but not used >> [-Wunused-but-set-variable] >> edit.cpp:146:8: warning: variable 'ins' set but not used >> [-Wunused-but-set-variable] >> edit.cpp: In static member function 'static void >> Edit::printQAlignNoCheck(std::ostream&, const char*, const BTDnaString&, >> const EList<Edit>&)': >> edit.cpp:180:8: warning: variable 'ins' set but not used >> [-Wunused-but-set-variable] >> edit.cpp:201:8: warning: variable 'ins' set but not used >> [-Wunused-but-set-variable] >> edit.cpp:222:8: warning: variable 'ins' set but not used >> [-Wunused-but-set-variable] >> edit.cpp: In static member function 'static void Edit::toRef(const >> BTDnaString&, const EList<Edit>&, BTDnaString&, bool, size_t, size_t)': >> edit.cpp:277:8: warning: variable 'ins' set but not used >> [-Wunused-but-set-variable] >> edit.cpp: In static member function 'static bool Edit::repOk(const >> EList<Edit>&, const BTDnaString&, bool, size_t, size_t)': >> edit.cpp:358:8: warning: variable 'del' set but not used >> [-Wunused-but-set-variable] >> edit.cpp:358:21: warning: variable 'ins' set but not used >> [-Wunused-but-set-variable] >> edit.cpp:358:34: warning: variable 'mm' set but not used >> [-Wunused-but-set-variable] >> In file included from bt2_idx.h:45:0, >> from bt2_idx.cpp:25: >> word_io.h: In function 'uint32_t readU32(int, bool)': >> word_io.h:86:27: error: 'read' was not declared in this scope >> word_io.h: In function 'uint32_t readI32(int, bool)': >> word_io.h:134:27: error: 'read' was not declared in this scope >> In file included from bt2_idx.h:47:0, >> from bt2_idx.cpp:25: >> ref_read.h: In constructor 'RefRecord::RefRecord(int, bool)': >> ref_read.h:69:21: error: 'read' was not declared in this scope >> In file included from bt2_idx.cpp:25:0: >> bt2_idx.h: In destructor 'Ebwt::~Ebwt()': >> bt2_idx.h:927:3: error: 'close' was not declared in this scope >> bt2_idx.h:928:3: error: 'close' was not declared in this scope >> In file included from bt2_idx.h:45:0, >> from bt2_io.cpp:25: >> word_io.h: In function 'uint32_t readU32(int, bool)': >> word_io.h:86:27: error: 'read' was not declared in this scope >> word_io.h: In function 'uint32_t readI32(int, bool)': >> word_io.h:134:27: error: 'read' was not declared in this scope >> In file included from bt2_idx.h:47:0, >> from bt2_io.cpp:25: >> ref_read.h: In constructor 'RefRecord::RefRecord(int, bool)': >> ref_read.h:69:21: error: 'read' was not declared in this scope >> In file included from bt2_io.cpp:25:0: >> bt2_idx.h: In destructor 'Ebwt::~Ebwt()': >> bt2_idx.h:927:3: error: 'close' was not declared in this scope >> bt2_idx.h:928:3: error: 'close' was not declared in this scope >> bt2_io.cpp: In member function 'void Ebwt::readIntoMemory(int, int, bool, >> bool, bool, bool, EbwtParams*, bool, bool, bool)': >> bt2_io.cpp:61:28: error: 'close' was not declared in this scope >> bt2_io.cpp:69:29: error: 'close' was not declared in this scope >> bt2_io.cpp:268:34: error: 'lseek' was not declared in this scope >> bt2_io.cpp:282:59: error: 'read' was not declared in this scope >> bt2_io.cpp:316:44: error: 'lseek' was not declared in this scope >> bt2_io.cpp:329:70: error: 'read' was not declared in this scope >> bt2_io.cpp:340:43: error: 'lseek' was not declared in this scope >> bt2_io.cpp:348:42: error: 'lseek' was not declared in this scope >> bt2_io.cpp:378:71: error: 'read' was not declared in this scope >> bt2_io.cpp:397:43: error: 'lseek' was not declared in this scope >> bt2_io.cpp:417:31: error: 'lseek' was not declared in this scope >> bt2_io.cpp:443:43: error: 'lseek' was not declared in this scope >> bt2_io.cpp:451:66: error: 'read' was not declared in this scope >> bt2_io.cpp:473:44: error: 'lseek' was not declared in this scope >> bt2_io.cpp:481:74: error: 'read' was not declared in this scope >> bt2_io.cpp:500:42: error: 'lseek' was not declared in this scope >> bt2_io.cpp:516:44: error: 'read' was not declared in this scope >> bt2_io.cpp:575:60: error: 'read' was not declared in this scope >> bt2_io.cpp:596:45: error: 'lseek' was not declared in this scope >> bt2_io.cpp:608:59: error: 'read' was not declared in this scope >> bt2_io.cpp:617:71: error: 'read' was not declared in this scope >> bt2_io.cpp:640:45: error: 'lseek' was not declared in this scope >> bt2_io.cpp:660:27: error: 'lseek' was not declared in this scope >> In file included from bt2_idx.h:45:0, >> from bt2_util.cpp:26: >> word_io.h: In function 'uint32_t readU32(int, bool)': >> word_io.h:86:27: error: 'read' was not declared in this scope >> word_io.h: In function 'uint32_t readI32(int, bool)': >> word_io.h:134:27: error: 'read' was not declared in this scope >> In file included from bt2_idx.h:47:0, >> from bt2_util.cpp:26: >> ref_read.h: In constructor 'RefRecord::RefRecord(int, bool)': >> ref_read.h:69:21: error: 'read' was not declared in this scope >> In file included from bt2_util.cpp:26:0: >> bt2_idx.h: In destructor 'Ebwt::~Ebwt()': >> bt2_idx.h:927:3: error: 'close' was not declared in this scope >> bt2_idx.h:928:3: error: 'close' was not declared in this scope >> In file included from ref_read.h:32:0, >> from reference.h:32, >> from reference.cpp:21: >> word_io.h: In function 'uint32_t readU32(int, bool)': >> word_io.h:86:27: error: 'read' was not declared in this scope >> word_io.h: In function 'uint32_t readI32(int, bool)': >> word_io.h:134:27: error: 'read' was not declared in this scope >> In file included from reference.h:32:0, >> from reference.cpp:21: >> ref_read.h: In constructor 'RefRecord::RefRecord(int, bool)': >> ref_read.h:69:21: error: 'read' was not declared in this scope >> reference.cpp: In constructor 'BitPairReference::BitPairReference(const >> string&, bool, bool, EList<std::basic_string<char> >*, EList<SString<char> >> >*, bool, bool, bool, bool, bool, bool)': >> reference.cpp:181:2: error: 'close' was not declared in this scope >> make[1]: *** [bowtie2-build] Error 1 >> > The full build log is available from: > > http://people.debian.org/~lucas/logs/2012/05/08/bowtie2_2.0.0-beta5-1_unstable.log > > A list of current common problems and possible solutions is available at > http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! > > About the archive rebuild: The rebuild was done on about 50 AMD64 nodes > of the Grid'5000 platform, using a clean chroot. Internet was not > accessible from the build systems. > > > > _______________________________________________ > Debian-med-packaging mailing list > debian-med-packag...@lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > Hello,
Thank you for reporting. The problem was related to gcc4.7 - missing unistd.h include. The fix is available in git repository. http://anonscm.debian.org/gitweb/?p=debian-med/bowtie2.git Will try to upload it after a review. Best regards, Alex -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
